Repitools: Epigenomic tools
Version 1.22.0

Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

AuthorMark Robinson <mark.robinson@imls.uzh.ch>, Dario Strbenac <dario.strbenac@sydney.edu.au>, Aaron Statham <a.statham@garvan.org.au>, Andrea Riebler <andrea.riebler@math.ntnu.no>
Bioconductor views DNAMethylation GeneExpression MethylSeq
Date of publicationNone
MaintainerMark Robinson <mark.robinson@imls.uzh.ch>
LicenseLGPL (>= 2)
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Repitools")

Popular man pages

absoluteCN: Calculate and Segment Absolute Copy Number from Sequencing...
annotationLookup: Forms a mapping between probes on a tiling array and windows...
BAM2GRanges: Read in a (list of) BAM file(s) into a GRanges(List) object.
binPlots: Create line plots of averaged signal across a promoter
cpgDensityCalc: Calculate CpG Density in a Window
mappabilityCalc: Calculate The Mappability of a Region
mergeReplicates: Merge GRanges that are of replicate experiments.
See all...

All man pages Function index File listing

Man pages

abcdDNA: A wrapper for fitting the offset-adjusted ABCD-DNA GLM
absoluteCN: Calculate and Segment Absolute Copy Number from Sequencing...
AdjustedCopyEstimate-class: Container for results of GC adjusted copy number estimation.
AffymetrixCdfFile-class: Placeholder For AffymetrixCdfFile Documentation
AffymetrixCelSet-class: Placeholder For AffymetrixCelSet Documentation
annoDF2GR: Convert a 'data.frame' to a 'GRanges'.
annoGR2DF: Convert an annotated 'GRanges' to a 'data.frame'.
annotationBlocksCounts: Counts the number of sequencing reads within supplied genomic...
annotationBlocksLookup: Forms a mapping between probe locations and chromosomal...
annotationCounts: Counts the number of sequencing reads surrounding supplied...
annotationLookup: Forms a mapping between probes on a tiling array and windows...
BAM2GRanges: Read in a (list of) BAM file(s) into a GRanges(List) object.
BayMethList-class: Class '"BayMethList"'
binPlots: Create line plots of averaged signal across a promoter
blocksStats: Calculate statistics for regions in the genome
checkProbes: Check Probe Specificity for Some Regions
chr21genes: Positions of Genes on Human Chromosome 21
ChromaBlocks: A function to find areas of enrichment in sequencing data
ChromaResults-class: ChromaResults class
chromosomeCNplots: Plot copy number by chromosome
ClusteredScoresList-class: Container for coverage matrices with clustering results.
clusterPlots: Visualisation of tables of feature coverages.
CopyEstimate-class: Container for results of fold change copy number estimation.
cpgBoxPlots: Boxplots of intensity, binned by Cpg Density
cpgDensityCalc: Calculate CpG Density in a Window
cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.
determineOffset: Function to determine the normalising offset f that accounts...
empBayes: Function to calculate prior parameters using empirical Bayes.
enrichmentCalc: Calculate sequencing enrichment
enrichmentPlot: Plot the distribution of sequencing enrichment.
expr: Vector of expression differences
FastQC-class: FastQC and associated classes
featureBlocks: Make windows for distances around a reference point.
featureScores: Get scores at regular sample points around genomic features.
findClusters: Find Clusters Epigenetically Modified Genes
GCadjustCopy: Calculate Absolute Copy Number from Sequencing Counts
GCAdjustParams-class: Container for parameters for mappability and GC content...
GCbiasPlots: Plot GC content vs. Read Counts Before Normalising, and GC...
gcContentCalc: Calculate The gcContent of a Region
genomeBlocks: Creates bins across a genome.
genQC: Plot Quality Checking Information for Sequencing Data
getProbePositionsDf: Translate Affymetrix probe information in a table.
getSampleOffsets: Calculates the sample-specific offsets, using the neutral...
hcRegions: Masking files for hg19
hyper: Gaussian hypergeometric function for vectorial arguments
loadPairFile: A routine to read Nimblegen tiling array intensities
loadSampleDirectory: A routine to read Nimblegen tiling array intensities
makeWindowLookupTable: Using the output of 'annotationLookup', create a tabular...
mappabilityCalc: Calculate The Mappability of a Region
MappabilitySource-class: Superclass for datatypes that can refer to genome mappability...
maskOut: Function to mask suspicious regions.
mergeReplicates: Merge GRanges that are of replicate experiments.
methylEst: Function to derive regional methylation estimates.
multiHeatmap: Superfigure plots
plotClusters: Plot Scores of Cluster Regions
plotQdnaByCN: Plotting the response of qDNA-seq data by CNV
processNDF: Reads in a Nimblegen microarray design file (NDF)
profilePlots: Create line plots of averaged signal across a promoter for...
QdnaData: A container for quantitative DNA sequencing data for ABCD-DNA...
regionStats: Find Regions of significance in microarray data
relativeCN: Calculate and Segment Relative Copy Number From Sequencing...
samplesList: Short Reads from Cancer and Normal
ScoresList-class: Container for 'featureScores()' output.
sequenceCalc: Find occurences of a DNA pattern
setCNVOffsets: Set the CNVOffsets of a 'QdnaData' object
summarizeScores: Subtract scores of different samples.
writeWig: Writes sequencing data out into wiggle files

Functions

AdjustedCopyEstimate Man page
AdjustedCopyEstimate,numeric,GRanges,numeric,numeric,matrix,list Man page
AdjustedCopyEstimate-class Man page
AffymetrixCdfFile Man page
AffymetrixCdfFile-class Man page
AffymetrixCelSet Man page
AffymetrixCelSet-class Man page
BAM2GRanges Man page
BAM2GRanges,character-method Man page
BAM2GRangesList Man page
BAM2GRangesList,character-method Man page
Basic_Statistics Man page
Basic_Statistics,FastQC-method Man page
Basic_Statistics,SequenceQC-method Man page
Basic_Statistics,SequenceQCSet-method Man page
BayMethList Man page
BayMethList,GRanges,matrix,matrix,numeric-method Man page
BayMethList-class Man page
ChromaBlocks Man page
ChromaBlocks,GRangesList,GRangesList-method Man page
ChromaResults Man page
ChromaResults-class Man page
ClusteredScoresList Man page
ClusteredScoresList,ScoresList-method Man page
ClusteredScoresList-class Man page
CopyEstimate Man page
CopyEstimate,GRanges,matrix,GRangesList,character-method Man page
CopyEstimate-class Man page
FDRTable Man page
FDRTable,ChromaResults-method Man page
FastQC-class Man page
GCAdjustParams Man page
GCAdjustParams,BSgenome,MappabilitySource-method Man page
GCAdjustParams-class Man page
GCadjustCopy Man page
GCadjustCopy,GRanges,matrix,GCAdjustParams-method Man page
GCadjustCopy,data.frame,matrix,GCAdjustParams-method Man page
GCbiasPlots Man page
GCbiasPlots,AdjustedCopyEstimate-method Man page
MappabilitySource Man page
MappabilitySource-class Man page
MismatchTable Man page
MismatchTable,SequenceQC-method Man page
MismatchTable,SequenceQCSet-method Man page
Mismatches Man page
Mismatches,SequenceQC-method Man page
Mismatches,SequenceQCSet-method Man page
Overrepresented_sequences Man page
Overrepresented_sequences,FastQC-method Man page
Overrepresented_sequences,SequenceQC-method Man page
Overrepresented_sequences,SequenceQCSet-method Man page
Per_base_GC_content Man page
Per_base_GC_content,FastQC-method Man page
Per_base_GC_content,SequenceQC-method Man page
Per_base_GC_content,SequenceQCSet-method Man page
Per_base_N_content Man page
Per_base_N_content,FastQC-method Man page
Per_base_N_content,SequenceQC-method Man page
Per_base_N_content,SequenceQCSet-method Man page
Per_base_sequence_content Man page
Per_base_sequence_content,FastQC-method Man page
Per_base_sequence_content,SequenceQC-method Man page
Per_base_sequence_content,SequenceQCSet-method Man page
Per_base_sequence_quality Man page
Per_base_sequence_quality,FastQC-method Man page
Per_base_sequence_quality,SequenceQC-method Man page
Per_base_sequence_quality,SequenceQCSet-method Man page
Per_sequence_GC_content Man page
Per_sequence_GC_content,FastQC-method Man page
Per_sequence_GC_content,SequenceQC-method Man page
Per_sequence_GC_content,SequenceQCSet-method Man page
Per_sequence_quality_scores Man page
Per_sequence_quality_scores,FastQC-method Man page
Per_sequence_quality_scores,SequenceQC-method Man page
Per_sequence_quality_scores,SequenceQCSet-method Man page
QdnaData Man page Source code
QdnaData-class Man page
RegionStats-class Man page
ScoresList Man page
ScoresList-class Man page
SequenceQC-class Man page
SequenceQCSet Man page
SequenceQCSet-class Man page
Sequence_Duplication_Levels Man page
Sequence_Duplication_Levels,FastQC-method Man page
Sequence_Duplication_Levels,SequenceQC-method Man page
Sequence_Duplication_Levels,SequenceQCSet-method Man page
Sequence_Length_Distribution Man page
Sequence_Length_Distribution,FastQC-method Man page
Sequence_Length_Distribution,SequenceQC-method Man page
Sequence_Length_Distribution,SequenceQCSet-method Man page
[,BayMethList,ANY,missing,ANY-method Man page
[,ClusteredScoresList,ANY,missing,ANY-method Man page
[,ScoresList,ANY,missing,ANY-method Man page
[,SequenceQCSet,ANY,missing,ANY-method Man page
abcdDNA Man page Source code
absoluteCN Man page
absoluteCN,GRanges,matrix,GCAdjustParams-method Man page
absoluteCN,data.frame,matrix,GCAdjustParams-method Man page
annoDF2GR Man page
annoDF2GR,data.frame-method Man page
annoGR2DF Man page
annoGR2DF,GRanges-method Man page
annotationBlocksCounts Man page
annotationBlocksCounts,ANY,data.frame-method Man page
annotationBlocksCounts,GRanges,GRanges-method Man page
annotationBlocksCounts,GRangesList,GRanges-method Man page
annotationBlocksCounts,character,GRanges-method Man page
annotationBlocksLookup Man page
annotationBlocksLookup,data.frame,GRanges-method Man page
annotationBlocksLookup,data.frame,data.frame-method Man page
annotationCounts Man page
annotationCounts,ANY,GRanges-method Man page
annotationCounts,ANY,data.frame-method Man page
annotationLookup Man page
annotationLookup,data.frame,GRanges-method Man page
annotationLookup,data.frame,data.frame-method Man page
belongsTo Source code
binPlots Man page
binPlots,ScoresList-method Man page
blocks Man page
blocks,ChromaResults-method Man page
blocksStats Man page
blocksStats,ANY,GRanges-method Man page
blocksStats,ANY,data.frame-method Man page
checkProbes Man page
checkProbes,GRanges,GRanges-method Man page
checkProbes,data.frame,data.frame-method Man page
chr21genes Man page
chromosomeCNplots Man page
chromosomeCNplots,AdjustedCopyEstimate-method Man page
chromosomeCNplots,CopyEstimate-method Man page
class:ChromaResults Man page
class:FastQC Man page
class:QdnaData Man page
class:RegionStats Man page
class:SequenceQC Man page
class:SequenceQCSet Man page
clusterPlots Man page
clusterPlots,ClusteredScoresList-method Man page
clusterPlots,ScoresList-method Man page
clusters Man page
clusters,ClusteredScoresList-method Man page
control Man page
control,BayMethList-method Man page
control<- Man page
control<-,BayMethList-method Man page
cpgBoxplots Man page Source code
cpgBoxplots,AffymetrixCelSet-method Man page
cpgBoxplots,matrix-method Man page
cpgDens Man page
cpgDens,BayMethList-method Man page
cpgDens<- Man page
cpgDens<-,BayMethList-method Man page
cpgDensityCalc Man page
cpgDensityCalc,GRanges,BSgenome-method Man page
cpgDensityCalc,GRangesList,BSgenome-method Man page
cpgDensityCalc,data.frame,BSgenome-method Man page
cpgDensityPlot Man page
cpgDensityPlot,GRangesList-method Man page
createBins Source code
cutoff Man page
cutoff,ChromaResults-method Man page
determineOffset Man page Source code
diracBetaDirac Source code
dlogit Source code
doBiasPlot Source code
doChrPlot Source code
drawSegs Source code
empBayes Man page Source code
enrichmentCalc Man page
enrichmentCalc,GRanges-method Man page
enrichmentCalc,GRangesList-method Man page
enrichmentPlot Man page
enrichmentPlot,GRangesList-method Man page
eqn2 Source code
eqn3 Source code
expr Man page
fOffset Man page
fOffset,BayMethList-method Man page
fOffset<- Man page
fOffset<-,BayMethList-method Man page
fdrTable Source code
featureBlocks Man page
featureBlocks,GRanges-method Man page
featureBlocks,data.frame-method Man page
featureScores Man page
featureScores,ANY,GRanges-method Man page
featureScores,ANY,data.frame-method Man page
findClusters Man page Source code
gcContentCalc Man page
gcContentCalc,GRanges,BSgenome-method Man page
gcContentCalc,data.frame,BSgenome-method Man page
genQC Man page
genQC,SequenceQCSet-method Man page
genQC,character-method Man page
genomeBlocks Man page
genomeBlocks,BSgenome-method Man page
genomeBlocks,numeric-method Man page
getBed Source code
getCpu Source code
getNames Source code
getProbePositionsDf Man page
getProbePositionsDf,AffymetrixCdfFile-method Man page
getQuantile Source code
getRegions Source code
getRegionsChr Source code
getSampleOffsets Man page Source code
getcredible Source code
getcredibleDBD Source code
hcRegions Man page
hyperg2F1_vec Man page Source code
length Man page
length,BayMethList-method Man page
length,ScoresList-method Man page
loadPairFile Man page Source code
loadSampleDirectory Man page Source code
logit Source code
makeClusters Source code
makeImageRect Source code
makeWindowLookupTable Man page Source code
mappabilityBSGenome Source code
mappabilityBigWig Source code
mappabilityCalc Man page
mappabilityCalc,GRanges,MappabilitySource-method Man page
mappabilityCalc,data.frame,MappabilitySource-method Man page
mappabilityFASTA Source code
marg Source code
margDirac Source code
margDirac_fB Source code
margDirac_fW Source code
maskEmpBayes Man page
maskEmpBayes,BayMethList-method Man page
maskEmpBayes<- Man page
maskEmpBayes<-,BayMethList-method Man page
maskOut Man page Source code
mergeReplicates Man page
mergeReplicates,GRangesList-method Man page
methEst Man page
methEst,BayMethList-method Man page
methEst<- Man page
methEst<-,BayMethList-method Man page
methylEst Man page Source code
methylEstDBD Source code
methylEstbeta Source code
multiHeatmap Man page Source code
mycdf Source code
mydmarginal Source code
mydmarginalDBD Source code
myhpd Source code
myoptimize Source code
myoptimizeDirac Source code
myquantile Source code
names,ScoresList-method Man page
names<-,ScoresList-method Man page
ncontrol Man page
ncontrol,BayMethList-method Man page
neqn Source code
neqn2 Source code
nsampleInterest Man page
nsampleInterest,BayMethList-method Man page
nvlogit Source code
plotClusters Man page
plotClusters,GRanges-method Man page
plotClusters,data.frame-method Man page
plotFreqs Source code
plotQdnaByCN Man page Source code
priorTab Man page
priorTab,BayMethList-method Man page
priorTab<- Man page
priorTab<-,BayMethList-method Man page
processNDF Man page Source code
profilePlots Man page
profilePlots,ScoresList-method Man page
readFastQC Man page Source code
regionStats Man page Source code
regionStats,AffymetrixCelSet-method Man page
regionStats,matrix-method Man page
regions Man page
regions,ChromaResults-method Man page
relativeCN Man page
relativeCN,GRanges,matrix-method Man page
relativeCN,data.frame,matrix-method Man page
sampleInterest Man page
sampleInterest,BayMethList-method Man page
sampleInterest<- Man page
sampleInterest<-,BayMethList-method Man page
samplesList Man page
scoreIntensity Source code
sequenceCalc Man page
sequenceCalc,GRanges,BSgenome-method Man page
sequenceCalc,data.frame,BSgenome-method Man page
setCNVOffsets Man page Source code
show,AdjustedCopyEstimate-method Man page
show,BayMethList-method Man page
show,ChromaResults-method Man page
show,ClusteredScoresList-method Man page
show,CopyEstimate-method Man page
show,FastQC-method Man page
show,QdnaData-method Man page
show,RegionStats-method Man page
show,ScoresList-method Man page
show,SequenceQC-method Man page
show,SequenceQCSet-method Man page
subsetRows Man page
subsetRows,ClusteredScoresList-method Man page
subsetRows,ScoresList-method Man page
summarizeScores Man page
summarizeScores,ScoresList,matrix-method Man page
tables Man page
tables,ScoresList-method Man page
windows Man page
windows,BayMethList-method Man page
windows<- Man page
windows<-,BayMethList-method Man page
writeWig Man page
writeWig,AffymetrixCelSet-method Man page
writeWig,GRangesList-method Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/BAM2GRanges.R
R/ChromaBlocks.R
R/FastQC-class.R
R/GCadjustCopy.R
R/GCbiasPlots.R
R/abcdDNA.R
R/absoluteCN.R
R/annoDF2GR.R
R/annoGR2DF.R
R/annotationLookup.R
R/binPlots.R
R/blocksStats.R
R/checkProbes.R
R/chromosomeCNplots.R
R/classes.R
R/clusterPlots.R
R/cpgBoxplots.R
R/cpgDensityCalc.R
R/cpgDensityPlot.R
R/determineOffset.R
R/empBayes.R
R/enrichmentCalc.R
R/enrichmentPlot.R
R/featureBlocks.R
R/featureScores.R
R/findClusters.R
R/gcContentCalc.R
R/genQC.R
R/genomeBlocks.R
R/getProbePositionsDf.R
R/hyper.R
R/makeWindowLookup.R
R/mappabilityCalc.R
R/maskOut.R
R/mergeReplicates.R
R/methylEst.R
R/multiHeatmap.R
R/plotClusters.R
R/processNimblegenArrays.R
R/profilePlots.R
R/regionStats.R
R/relativeCN.R
R/sequenceCalc.R
R/summarizeScores.R
R/utils.R
R/writeWig.R
build
build/vignette.rds
data
data/chr21genes.csv
data/datalist
data/expr.RData
data/hcRegions.RData
data/samplesList.RData
inst
inst/CITATION
inst/doc
inst/doc/Repitools_vignette.R
inst/doc/Repitools_vignette.Rnw
inst/doc/Repitools_vignette.pdf
inst/examples
inst/examples/annotationCounts_seq.R
inst/examples/binPlots_affy.R
inst/examples/binPlots_seq.R
inst/examples/blockStats_affy.R
inst/examples/clusterPlots_seq.R
inst/examples/cpgDensityPlot_seq.R
inst/examples/enrichmentPlot_seq.R
inst/examples/featureScores_array.R
inst/examples/featureScores_seq.R
inst/examples/findClusters_dataframe.R
inst/examples/mergeReplicates_seq.R
inst/examples/regionStats_affy.R
man
man/AdjustedCopyEstimate-class.Rd
man/AffymetrixCdfFile-class.Rd
man/AffymetrixCelSet-class.Rd
man/BAM2GRanges.Rd
man/BayMethList-class.Rd
man/ChromaBlocks.Rd
man/ChromaResults-class.Rd
man/ClusteredScoresList-class.Rd
man/CopyEstimate-class.Rd
man/FastQC-class.Rd
man/GCAdjustParams-class.Rd
man/GCadjustCopy.Rd
man/GCbiasPlots.Rd
man/MappabilitySource-class.Rd
man/QdnaData.Rd
man/ScoresList-class.Rd
man/abcdDNA.Rd
man/absoluteCN.Rd
man/annoDF2GR.Rd
man/annoGR2DF.Rd
man/annotationBlocksCounts.Rd
man/annotationBlocksLookup.Rd
man/annotationCounts.Rd
man/annotationLookup.Rd
man/binPlots.Rd
man/blocksStats.Rd
man/checkProbes.Rd
man/chr21genes.Rd
man/chromosomeCNplots.Rd
man/clusterPlots.Rd
man/cpgBoxPlots.Rd
man/cpgDensityCalc.Rd
man/cpgDensityPlot.Rd
man/determineOffset.Rd
man/empBayes.Rd
man/enrichmentCalc.Rd
man/enrichmentPlot.Rd
man/expr.Rd
man/featureBlocks.Rd
man/featureScores.Rd
man/findClusters.Rd
man/gcContentCalc.Rd
man/genQC.Rd
man/genomeBlocks.Rd
man/getProbePositionsDf.Rd
man/getSampleOffsets.Rd
man/hcRegions.Rd
man/hyper.Rd
man/loadPairFile.Rd
man/loadSampleDirectory.Rd
man/makeWindowLookupTable.Rd
man/mappabilityCalc.Rd
man/maskOut.Rd
man/mergeReplicates.Rd
man/methylEst.Rd
man/multiHeatmap.Rd
man/plotClusters.Rd
man/plotQdnaByCN.Rd
man/processNDF.Rd
man/profilePlots.Rd
man/regionStats.Rd
man/relativeCN.Rd
man/samplesList.Rd
man/sequenceCalc.Rd
man/setCNVOffsets.Rd
man/summarizeScores.Rd
man/writeWig.Rd
src
src/Makevars
src/Makevars.win
src/Rexchange.h
src/const.c
src/hyp2f1.c
src/mconf.h
src/mtherr.c
tests
tests/tests.R
vignettes
vignettes/Repitools_vignette.Rnw
vignettes/analyses1.tex
vignettes/analyses2.tex
vignettes/clusterPlot.png
vignettes/datasets.tex
vignettes/qc-cpgPlot.pdf
vignettes/qc-enrPlot.pdf
vignettes/qc.tex
vignettes/readme.txt
vignettes/rock1.png
vignettes/sInfo.tex
vignettes/utilities.tex
vignettes/visualisations-binPlotsHeatmap.pdf
vignettes/visualisations-binPlotsLine.pdf
vignettes/visualisations-cluPlots3.pdf
vignettes/visualisations-profPlots.pdf
vignettes/visualisations.tex
Repitools documentation built on May 20, 2017, 10:29 p.m.

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